Add options to generate violin plots instead of boxplots
Add support for Jenks natural breaks and custom grouping to step7TopGenesSurvival
Add support for custom regions and MotifDb filtering options to step7LinkedDNAMethylationSitesMotifSearching
step7TopGenesUserPeakOverlap now accepts peak names, generates results for each individual peak rather than each peak file, and accepts multiple input objects or directories
External genomic region files can now be provided as a list of multiple files and/or directories containing them, not just a directory
Fix TENETSavedSizePlot bug that caused warnings and failure to respect an explicitly specified size
Fix TENETCacheAllData to fail if any dataset does not exist on the hub
Significant documentation improvements
Do not suggest installing the development version of Bioconductor to use the stable version of the package, since it is no longer necessary
Update installation instructions for Ubuntu 24.04 and add a missing required package
Add a dependency on ggplot2 4.0 because the example MultiAssayExperiment object now requires it
Add CITATION file